MAD: no visible global function definition for ‘mad’
addTip: no visible global function definition for ‘head’
addTip: no visible global function definition for ‘runif’
check.Markers: no visible global function definition for ‘par’
check.Markers: no visible global function definition for ‘barplot’
check.Markers: no visible global function definition for ‘text’
dbReadTaxonomy: no visible global function definition for ‘head’
esearch: no visible global function definition for ‘browseURL’
filter.alignment : NNmean: no visible global function definition for
  ‘median’
megapteraHeatmap: no visible global function definition for ‘pdf’
megapteraHeatmap: no visible global function definition for ‘par’
megapteraHeatmap: no visible global function definition for ‘image’
megapteraHeatmap: no visible global function definition for ‘mtext’
megapteraHeatmap: no visible global function definition for ‘dev.off’
ncbiLineage: no visible global function definition for ‘head’
nucleotideOverlap: no visible global function definition for ‘tail’
sortRanks: no visible global function definition for ‘head’
sortRanks: no visible global function definition for ‘tail’
splitGiTaxon: no visible global function definition for ‘tail’
splitGiTaxon: no visible global function definition for ‘head’
stepA: no visible global function definition for ‘packageDescription’
stepB: no visible global function definition for ‘packageDescription’
stepB: no visible global function definition for ‘tail’
stepC: no visible global function definition for ‘packageDescription’
stepD: no visible global function definition for ‘packageDescription’
stepD: no visible global function definition for ‘head’
stepE: no visible global function definition for ‘packageDescription’
stepE: no visible global function definition for ‘head’
stepF: no visible global function definition for ‘packageDescription’
stepG: no visible global function definition for ‘packageDescription’
stepG: no visible binding for global variable ‘head’
stepG: no visible binding for global variable ‘tail’
stepH: no visible global function definition for ‘packageDescription’
supermatrix: no visible global function definition for ‘zip’
tax2tree: no visible global function definition for ‘formula’
whereToInsert: no visible global function definition for ‘head’
show,megapteraProj: no visible global function definition for ‘head’
show,taxon: no visible global function definition for ‘head’
Undefined global functions or variables:
  barplot browseURL dev.off formula head image mad median mtext
  packageDescription par pdf runif tail text zip
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "barplot", "image", "mtext", "par", "text")
  importFrom("stats", "formula", "mad", "median", "runif")
  importFrom("utils", "browseURL", "head", "packageDescription", "tail",
             "zip")
to your NAMESPACE file.